Digital Protein Biophysics of Aggregation

Proteins are the fundamental building blocks of life, underpinning functional processes in living systems. They are able to exert their biological activities by binding to other proteins to form functional complexes which act as the machinery of life. In certain cases, however, proteins escape cellular quality control mechanisms and form aberrant complexes. The formation of such clusters stabilised by inter-molecular hydrogen bonds, amyloid aggregates, has dramatic consequences for biological systems and they are implicated in neurodegenerative disorders. The fundamental biophysical chemistry governing the formation of protein clusters has been challenging to probe and understand as this process results in a highly heterogeneous distribution of aggregates of different sizes and with different properties, and correspondingly diverse effects on living cells’ function. As such, conventional bulk methods are challenging to apply to uncover a fundamental biophysical understanding of their formation, dynamics and behaviour. The present proposal addresses this fundamental problem by bringing together microfluidics and single molecule spectroscopy to develop a novel digital biophysics platform for studying protein aggregation. Through this route, we will be able to study aggregates one by one, inside and outside cells, and discover the fundamental physical determinants that govern their formation and effects on the cellular systems. This proposal is motivated by the hypothesis that the physico-chemical properties of protein aggregates modulate their biological activity, and by studying protein aggregation at the level of single aggregates and single cells, we will access fundamentally new biophysical chemistry, including how liquid-liquid phase separation can modulate the nucleation barriers in protein aggregation, what the molecular mechanisms are by which amyloid aggregates can self-multiply, and what physical parameters determine their effects on living cells.